SWISS-MODEL Repository - Model Details

Model Overview
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1
1054

Sequence
UniProt P12683
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P12683: 4932.YML075C

Domain
Link to: [ InterPro ]
HMG-CoA_red
Sterol-sensing
HPIH

Model 3D Structure
Model information:
Modelled residue range: 644 to 1015
Based on template: [ 2q1l ]  
Sequence Identity [%]: 61%
Model date: 2013-02-19
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2q1l): TETRAMER

Ligand information: [details]
Ligands in the template: 882: 2.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment

TARGET    1                             RAVAVRRK ALSILAEAPV LASDRLPYKN
2q1lA     459   akflsdaeii qlvnaiethe --rgvsirrq llskklseps -slqylpyrd
                                                                      
TARGET                                   hhhhhhh hhhh                 
2q1lA                hhhhh hhhh     h   hhhhhhhh hhhh                 


TARGET    29    YDYDRVFGAC CENVIGYMPL PVGVIGPLVI DGTSYHIPMA TTEGCLVASA
2q1lA     517   ynyslvmgac cenvigympi pvgvagplcl dekefqvpma ttegclvast
                                                                      
TARGET             hhh                sssss  sss   sss ssss s    hhhhh
2q1lA              hhh                sssss  sss   sss ssss s    hhhhh


TARGET    79    MRGCKAINAG GGATTVLTKD GMTRGPVVRF PTLKRSGACK IWLDSEEGQN
2q1lA     567   nrgcraiglg ggassrvlad gmtrgpvvrl pracdsaevk awletsegfa
                                                                      
TARGET          hhhhhhhhh     sssssss ssssssssss   hhhhhhhh hhh   hhhh
2q1lA           hhhhhhhhh     sssssss ssssssssss   hhhhhhhh hhh   hhhh


TARGET    129   AIKKAFNSTS RFARLQHIQT CLAGDLLFMR FRTTTGDAMG MNMISKGVEY
2q1lA     617   vikeafdsts rfarlqklht siagrnlyir fqsrsgdamg mnmiskgtek
                                                                      
TARGET          hhhhhhhh           ss sss ssssss sss        hhhhhhhhhh
2q1lA           hhhhhhhh           ss sss ssssss sss        hhhhhhhhhh


TARGET    179   SLKQMVEEYG WEDMEVVSVS GNYCTDKKPA AINWIEGRGK SVVAEATIPG
2q1lA     667   alsklheyf- -pemqilavs gnyctdkkpa ainwiegrgk svvceavipa
                                                                      
TARGET          hhhhhhhhh      sss                hhhhh  ss ssssssss h
2q1lA           hhhhhhhh       sss                hhhhh  ss ssssssss h


TARGET    229   DVVRKVLKSD VSALVELNIA KNLVGSAMAG SVGGFNAHAA NLVTAVFLAL
2q1lA     715   kvvrevlktt teamievnin knlvgsamag siggynahaa nivtaiyiac
                                                                      
TARGET          hhhhhh     hhhhhhhhhh hhhhhhhhh    sss    h hhhhhhhhhh
2q1lA           hhhhhh     hhhhhhhhhh hhhhhhhhh    sss    h hhhhhhhhhh


TARGET    279   GQDPAQNVES SNCITLMKEV ---DGDLRIS VSMPSIEVGT IGGGTVLEPQ
2q1lA     765   gqdaaqnvgs sncitlmeas gptnedlyis ctmpsieigt vgggtnllpq
                                                                      
TARGET                 hhh   ssssssss      sssss sss               hhh
2q1lA                  hhh   ssssssss ss sssssss sss               hhh


TARGET    326   GAMLDLLGVR GPHATAPGTN ARQLARIVAC AVLAGELSLC AALAAGH   
2q1lA     815   qaclqmlgvq gackdnpgen arqlarivcg tvmagelslm aalaagh-  
                                                                      
TARGET          hhhhhhh            hh hhhhhhhhhh hhhhhhhhhh hhhhh     
2q1lA           hhhhhhh            hh hhhhhhhhhh hhhhhhhhhh hhhhh     



Quality


Template's ligands section
Ligands in the template: 882: 2.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.


Quaternary Structure Annotation of the Template
2q1l is annotated as TETRAMER
The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry
The following biological unit was used to build the template structure: 2q1l.pdb1.gz

Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template can be assumed to be similar (=TETRAMER)
The corresponding reliability score is 0.616 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 2q1lD


Template Selection
 - Start SMR-Pipeline for:9cd8da4e616e10125014c551e9ac98b9 on BC2-cluster at Tue Feb 19 02:00:31
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with C found
 - No template with B found
 - No template with A found
 - No template with C found
 - No template with B found
 - No template with A found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with D found
 - No template with A found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with D found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                  ****************************
 - building model based on 2q1lA (644-1015) was successful 
 -                                               *******************************
 - building model based on 2r4fC (600-1014) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:9cd8da4e616e10125014c551e9ac98b9 on BC2-cluster at Tue Feb 19 02:25:39
2013 




Template Description
Match Chain SeqId

3cct: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.12A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1013 3cctD 62%
[Model]

2r4f: SUBSTITUTED PYRAZOLES AS HEPATSELECTIVE HMG-COA REDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1014 2r4fD 62%
[Model]

3cda: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.07A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1013 3cdaD 62%
[Model]

3ccz: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1014 3cczD 62%
[Model]

3cdb: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1015 3cdbD 62%
[Model]

1hw8: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH COMPACTIN (ALSO KNOWN AS MEVASTATIN)
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1014 1hw8C 62%
[Model]
644-1013 1hw8D 62%
[Model]

2q1l: DESIGN AND SYNTHESIS OF PYRROLE-BASED, HEPATOSELECTIVE HMGCOA REDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.05A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

614-1015 2q1lB 60%
[Model]
644-1013 2q1lD 62%
[Model]
644-1015 2q1lA 62%
[Model]

3cd7: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.05A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

614-1015 3cd7B 60%
[Model]
644-1015 3cd7A 62%
[Model]
644-1013 3cd7D 62%
[Model]

3ccw: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1013 3ccwD 62%
[Model]

1hwi: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH FLUVASTATIN
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

630-1016 1hwiA 61%
[Model]
644-1014 1hwiD 62%
[Model]
644-1016 1hwiC 62%
[Model]

3cd0: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

644-1015 3cd0D 62%
[Model]

1hwl: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH ROSUVASTATIN (FORMALLY KNOWN AS ZD4522)
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

618-1014 1hwlC 60%
[Model]
618-1014 1hwlB 60%
[Model]
633-1014 1hwlD 61%
[Model]

1hwj: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH CERIVASTATIN
Solved by: X-RAY, Resolution: 2.26A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

615-1014 1hwjC 60%
[Model]
618-1014 1hwjB 60%
[Model]
634-1014 1hwjD 61%
[Model]

1hwk: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH ATORVASTATIN
Solved by: X-RAY, Resolution: 2.22A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

616-1015 1hwkA 60%
[Model]
633-1014 1hwkB 61%
[Model]
635-1014 1hwkD 61%
[Model]

1hw9: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH SIMVASTATIN
Solved by: X-RAY, Resolution: 2.33A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

618-1014 1hw9B 60%
[Model]
633-1014 1hw9C 61%
[Model]
633-1013 1hw9D 61%
[Model]

2q6b: DESIGN AND SYNTHESIS OF NOVEL, CONFORMATIONALLY RESTRICTEDHMG-COA REDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

614-1020 2q6bD 60%
[Model]

1dqa: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH HMG, COA, AND NADP+
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

616-1024 1dqaA 60%
[Model]
624-1025 1dqaC 61%
[Model]
631-1025 1dqaD 61%
[Model]
616-1020 1dqaB 60%
[Model]

1dq9: COMPLEX OF CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASE WITH HMG-COA
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

614-1020 1dq9C 60%
[Model]
614-1019 1dq9D 60%
[Model]
616-1019 1dq9A 60%
[Model]
614-1018 1dq9B 60%
[Model]

3cd5: THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COREDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.39A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

614-1018 3cd5D 60%
[Model]

1dq8: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASWITH HMG AND COA
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

614-1018 1dq8D 60%
[Model]
616-1019 1dq8B 60%
[Model]
618-1019 1dq8C 60%
[Model]

2q6c: DESIGN AND SYNTHESIS OF NOVEL, CONFORMATIONALLY RESTRICTEDHMG-COA REDUCTASE INHIBITORS
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

614-1015 2q6cD 60%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.




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